Email notifications from Messages and To-do comments does not seem to be sending out, even after checking username upon creation of message. I get my wordpress new user notifications. I have also checked my spam folder but they are not there.

I just checked and all notification is working fine. I think you got also notification message from demo. I think problem in not from our end. Maybe server issue or others. Thank you for understanding…

I'm using default email for sending.
The email plugins I was using is mainly for aesthetics, displaying custom name/from address.
– WP Mail From II
– WP Better Emails
– SB Welcome Email Editor
I tested with all these deactivated but the emails still does not seem to send out (only new user registration does, but I think that's more of wp's end).

Oops sorry it's working perfectly now without mandrill. I realized the update through WordPress -> Plugins did not work. I tried to run it several times but it still shows the old version and prompts for update. In the end, I did a ftp upload to replace the files.